Identification of pathogenic organisms, for example in a subject or the food supply, is a key first step in devising an informed, effective treatment strategy or protection of the food supply, respectively. For example, to effectively treat pathogen infection, it is advisable to begin treatment as early as possible in the in the development of the infection, ideally even before onset of severe clinical symptoms. Similarly, protection of the food supply may require early action to detect contamination with pathogenic organisms and effectively remove tainted or otherwise contaminated food from distribution channels, before large scale outbreaks of food poisoning.
Currently, microbiologic methods rely on growth of pathogens in culture, followed by subculture and biochemical assays to determine pathogen identity, a process that can take over 48 hours. Current efforts at molecular diagnostics have centered on DNA recognition through PCR amplification, or recognition of protein signatures through mass spectrometry. PCR-based techniques have the advantage of amplification of signal, potentially permitting earlier detection. However, polymerases used in PCR are relatively intolerant to the biochemical milieu of many laboratory samples, and may require processing steps that introduce delays. Further, the extrinsic amplification step introduces the possibility of false negative and positives as well. In turn, mass spectrometry is limited in recognition by the need to unambiguously recognize peptide signatures that have less inherent distinction from human or environmental material that may be present in a sample.
Accordingly, a need exists for a rapid method of detecting and identifying infectious disease pathogens. More rapid organism identification would permit informed decisions to be made earlier, for example treatment decisions. A test that provides sensitive, specific detection of pathogen types and subtypes in a relatively short time is needed, so that identification is completed in sufficient time to permit effective treatment of an infected person or removing tainted products from the food supply.